that's great to hear that you are reusing Mylyn in this way. We have indeed started working on improving the core/ui split to support use cases of this sort better. I would recommend taking a look at these two bugs:
The first one is about moving the connector extension point into the tasks.core bundle to enable discovery of connectors in headless contexts. The tasks framework would still require the extension registry so this would work best in OSGi environments but connectors could be used through the framework without the UI more easily.
The second change is about moving life-cycle management of repositories and the task list into a core bundle and exposing the data model as an OSGi service. This would allow headless clients to work with the default task list and repository instances which are currently only accessible from the UI. Another goal of the change is to extract the code for creating the model instance. This would allow clients to instantiate their own tasks model with separate connector instances, caches etc. more easily. Those model instance wouldn't interact with the Mylyn UI but still support all core functionality such as query synchronization.
It'd be great if you could comment on the bugs and let us know what your requirements are and help evaluate the proposed changes. Also, please feel encouraged to file new bugs if you have other requirements that aren't already captured in Bugzilla.
Steffen